This paper empirically examines the dynamic relationship between stock market volatility and commodity prices through the time-varying risk aversion channel using daily data between December 31 in 1999 and June 14 in 2021. We employ a time-varying structural-form vector autoregressive model (VAR) model with (aggregate, sectoral and sixteen individual) commodity prices. The results suggest that the transmission mechanism of stock market volatility shocks on the commodity prices change over time. The negative effect of stock market volatility on commodity prices is more statistically significant in the 2008–09 Global Financial Crisis than that during the COVID-19 pandemic in 2020. Further, the effect is greater in energy commodities compared to the agricultural and metals markets. The long-lasting negative effect of risk aversion is stronger compared to that of the expected stock market volatility on the commodity price. The change in the stock-commodity transmission mechanism is likely due to changes in underlying sources of risk aversion and expected uncertainty over time.